Garlic substrate could influence plant growth through affecting soil microbiome structure. The relationship mechanism between changes in soil microbial communities, diseases suppression and plant development, however, remains unclear, particularly in degraded soil micro-ecological environment. In this study, garlic substrates as a soil amendment was incorporated with different ratio (1:100, 3:100 and 5:100 g/100g of soil) in a replanted disturbed soil of long-term cucumber monoculture (annual double cropping system in a greenhouse). The results indicated that higher amount of C-amended garlic substrate significantly induced soil suppressiveness (35.9% greater than CK) against foliar disease incidence rate. This inhibitory effect consequently improved the cucumber growth performance and fruit yield to 20% higher as compared to non-amended soil. Short-term garlic substrate addition modified the soil quality through increase of soil organic matter (SOM), nutrients availability and enzymatic activities. Illumina MiSeq sequencing analysis revealed that soil bacterial and fungal communities in the garlic amendment were significantly different from control. Species richness and diversity indices significantly increased under treated soil. The correlation based heatmap analysis suggested that soil OM, nutrient contents and biological activators were the primary drivers of reshaping the microbial community structure. Furthermore, garlic substrate inhibited soil borne pathogen taxa (Fusarium and Nematoda) and their reduced abundances significantly affected the crop yield. In addition, host plant recruited certain plant-beneficial microbes due to substrate addition that could directly contribute in plant-pathogen inhibition and crop biomass production. For examples, abundant Acidobacteria, Ascomycota and Glomeromycota taxa were significantly associated with cucumber yield promotion. The Firmicutes, Actinobacteria, Bacteroidetes, Basidiomycota and Glomeromycota were the associated microbial taxa that possibly performed as antagonists of Fusarium wilt, having plant pathogens-suppression potentials in monocropped cucumber-planted soil.